@sjcrh/proteinpaint-client 2.219.1 → 2.220.0

package/dist/chunk-EYKJQJ7R.js

@@ -0,0 +1,382 @@
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  mclass
+} from "./chunk-WJLRU5OF.js";
+import {
+  copyMerge
+} from "./chunk-HBNB5TRH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/matrix/matrix.sorterUi.js
+var alphabet = `ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");
+function getSorterUi(opts) {
+  const { controls, holder } = opts;
+  const parent = controls.parent;
+  const s = structuredClone(parent.config.settings.matrix);
+  const l = s.controlLabels;
+  const tip = new Menu({ padding: "", parent_menu: parent.app.tip?.d.node() });
+  let input, theads = [], sectionData, dragged = {};
+  const self = {
+    dom: { tip },
+    opts,
+    highlightColor: "none",
+    label: `Sort ${l.Samples}`,
+    title: `Set how to sort ${l.samples}`,
+    type: "custom",
+    expanded: opts.expanded || false,
+    expandedSection: opts.expandedSection || "",
+    init(overrides = {}, _opts = {}) {
+      tip.clear().hide();
+      if (parent.config.settings.matrix != s) copyMerge(s, parent.config.settings.matrix);
+      if (s !== overrides) copyMerge(s, overrides);
+      self.settings = s;
+      self.activeOption = structuredClone(s.sortOptions[s.sortSamplesBy]);
+      sectionData = [
+        // TODO: add an advanced menu section here for sortBySampleAncestry = 'first'
+        {
+          label: `For each selected row, sort ${l.samples} by matching data`,
+          notDraggable: true,
+          tiebreakers: [],
+          handler: handleSelectedTerms
+        },
+        ...self.activeOption.sortPriority,
+        {
+          label: `Sort ${l.samples} by name, alphabetically`,
+          notDraggable: true,
+          tiebreakers: []
+        }
+      ];
+      Object.assign(opts, _opts);
+      opts.holder.selectAll("*").remove();
+      const topDiv = opts.holder.append("div").style("text-align", "right");
+      topDiv.append("button").html("Apply").on("click", apply);
+      topDiv.append("button").html("Reset").on("click", (event, d) => self.init());
+      const table = opts.holder.append("table");
+      const tr = table.append("thead");
+      tr.append("th").html("Priority").style("text-align", "left").style("max-width", "0px");
+      tr.append("th").html("Description");
+      tr.append("th").html("Action");
+      let i = 0, j = 0;
+      for (const sd of sectionData) {
+        const hasTbOrder = sd.tiebreakers?.[0]?.order || sd.handler;
+        const thead = table.append("thead").datum(sd).property("draggable", !sd.notDraggable).attr("droppable", true).on("dragstart", trackDraggedSection).on("dragover", highlightSection).on("dragleave", unhighlightSection).on("drop", adjustSortPriority);
+        theads.push(select_default(thead));
+        const tr2 = thead.append("tr").style("background-color", "#eee").on("mouseover", undoMouseoverHighlights);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("font-weight", 400).html(alphabet[j++]).on("click", hasTbOrder ? toggleSection : null);
+        const td2 = tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "left").style("cursor", hasTbOrder ? "pointer" : "").on("click", hasTbOrder ? toggleSection : null);
+        td2.append("span").style("margin-right", "12px").style("font-weight", 400).html(sd.label);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "center").style("font-weight", 400).style("cursor", hasTbOrder ? "pointer" : "").append("span").html(hasTbOrder ? "Details" : " ").on("click", hasTbOrder ? toggleSection : null);
+        const tbody = table.append("tbody").datum(sd).style("display", self.expandedSection == "all" || self.expandedSection == sd.label ? "" : "none");
+        for (const tb of sd.tiebreakers) {
+          if (tb.skip) continue;
+          if (!sd.types?.includes("geneVariant")) {
+            continue;
+          }
+          const tr3 = tbody.append("tr").on("mouseover", undoMouseoverHighlights).datum(tb).attr("draggable", !tb.disabled && sd.types?.length !== 0).attr("droppable", !tb.disabled && sd.types?.length !== 0).on("dragstart", trackDraggedTieBreaker).on("dragover", highlightTieBreaker).on("dragleave", unhighlightTieBreaker).on("drop", adjustTieBreakers);
+          if (!tb.disabled) i++;
+          const td1 = tr3.append("td").attr(
+            "title",
+            tb.disabled ? `This tiebreaker is currently not being used to sort ${l.cases}. Check the box to use.` : `The number indicates the order in which this tiebreaker is used. Unched the box to skip.`
+          ).datum(tb);
+          td1.style("padding", "5px").style("vertical-align", "top").style("text-align", "center");
+          td1.append("span").html(!tb.disabled ? i : "");
+          const td22 = tr3.append("td").style("opacity", tb.disabled ? 0.5 : 1).style("padding", "5px").style("vertical-align", "top").style("max-width", "500px");
+          td22.append("span").html(tb.label || "");
+          if (!tb.disabled) {
+            const label = td22.append("label");
+            label.append("span").html("<br>(use data list order ");
+            if (!tb.isOrdered) tb.isOrdered = false;
+            const checkbox = label.append("input").datum(tb).attr("type", "checkbox").property("checked", tb.isOrdered).style("vertical-align", "bottom").on("change", toggleTieBreakerIsOrdered);
+            label.append("span").html(")");
+            const order = tb.order;
+            td22.append("div").attr("class", "sjpp-matrix-sorter-ui-value").selectAll("div").data(
+              order.map((key, index) => ({
+                lstName: "order",
+                key,
+                cls: mclass[key],
+                tb,
+                dragstart: trackDraggedValue,
+                dragover: highlightValue,
+                dragleave: unhighlightValue,
+                drop: adjustValueOrder,
+                filterByClass: s.filterByClass,
+                index
+              }))
+            ).enter().append("div").style("display", tb.isOrdered ? "block" : "inline-block").each(setValueDiv);
+            if (tb.notUsed?.length) {
+              const notUsed = td22.append("div");
+              notUsed.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-add").style("display", "inline-block").style("padding", "5x").style("vertical-align", "top").style("padding", "3px 5px").style("cursor", "pointer").html(`+Add`).on("click", showNotUsedValues);
+            }
+          }
+          const td3 = tr3.append("td").style("text-align", "center").style("vertical-align", "top");
+          if (tb.mayToggle) {
+            td3.append("button").datum(tb).html(tb.disabled ? "Enable" : "Disable").on("click", toggleTieBreakerDisabled);
+          }
+        }
+        const lastTr = tbody.append("tr").attr("draggable", true).on("mouseover", undoMouseoverHighlights);
+        lastTr.append("td").html("&nbsp;");
+        const tdNew = lastTr.append("td").style("text-align", "left").html(sd.details && !sd.order?.length ? sd.details : "&nbsp;");
+        if (sd.handler) sd.handler(tdNew, lastTr, tbody);
+        lastTr.append("td").html("&nbsp;");
+      }
+    },
+    toggleSection,
+    trackDraggedSection,
+    highlightSection,
+    unhighlightSection,
+    adjustSortPriority,
+    trackDraggedTieBreaker,
+    highlightTieBreaker,
+    unhighlightTieBreaker,
+    adjustTieBreakers,
+    trackDraggedValue,
+    highlightValue,
+    unhighlightValue,
+    adjustValueOrder,
+    apply
+  };
+  function toggleSection(event, d = { label: "all" }) {
+    self.expandedSection = self.expandedSection === d.label ? "" : d.label;
+    self.expanded = !!self.expandedSection;
+    self.init();
+  }
+  function trackDraggedSection(event, d) {
+    dragged.type = "sortPriority";
+    dragged.data = d;
+    dragged.index = self.activeOption.sortPriority.indexOf(d);
+  }
+  function highlightSection(event, d) {
+    if (dragged.type != "sortPriority" || d == dragged.data) return;
+    event.preventDefault();
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("th").style(borderSide, "2px solid blue");
+  }
+  function unhighlightSection(event, d) {
+    if (dragged.type != "sortPriority") return;
+    event.preventDefault();
+    select_default(this).selectAll("th").style("border", "none");
+  }
+  function adjustSortPriority(event, d) {
+    if (d == dragged.data) return;
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    self.activeOption.sortPriority.splice(dragged.index, 1);
+    self.activeOption.sortPriority.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function trackDraggedTieBreaker(event, d) {
+    dragged.type = "tiebreaker";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.index = dragged.sectionData.tiebreakers.indexOf(d);
+  }
+  function highlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("td:nth-child(2)").style(borderSide, "2px solid blue");
+  }
+  function unhighlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker") return;
+    event.preventDefault();
+    select_default(this).selectAll("td:nth-child(2)").style("border", "none");
+  }
+  function toggleTieBreakerIsOrdered(event, tb) {
+    event.stopPropagation();
+    tb.isOrdered = !tb.isOrdered;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function toggleTieBreakerDisabled(event, tb) {
+    event.stopPropagation();
+    tb.disabled = !tb.disabled;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function adjustTieBreakers(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    dragged.sectionData.tiebreakers.splice(dragged.index, 1);
+    dragged.sectionData.tiebreakers.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function setValueDiv(d) {
+    const title = [];
+    if (d.tb.notUsed?.includes(d.key)) title.push(`- Click on this label to include in used data values.`);
+    if (d.filterByClass[d.key])
+      title.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");
+    if (title.length) title.unshift(`To use this data value for sorting ${l.samples}:`);
+    const skipped = d.tb.notUsed?.includes(d.key);
+    const opacity = d.filterByClass[d.key] == "value" ? 0.5 : 1;
+    const div = select_default(this).attr("aria-label", title.length ? title.join("\n") : `Click to not use this data value to sort ${l.samples}`).attr("draggable", d.tb.isOrdered ? true : false).attr("droppable", d.tb.isOrdered ? true : false).style("width", "fit-content").style("margin-right", "10px").style("overflow", "hidden").style("white-space", "nowrap").style("opacity", opacity).style("cursor", "pointer").on("dragstart", d.dragstart).on("dragover", d.dragover).on("dragleave", d.dragleave).on("drop", d.drop).on("mouseenter", () => toggle.style("opacity", 1)).on("mouseleave", () => toggle.style("opacity", 0)).on("click", () => {
+      if (title.length) {
+        const cls = "sjpp-matrix-sorter-value-note";
+        div.selectAll(`.${cls}`).remove();
+        const note = div.append("div").attr("class", cls).style("max-width", "200px").style("padding", "5px");
+        note.html(title.join("<br>"));
+        if (d.filterByClass[d.key]) return;
+      }
+      const targetLstName = d.lstName == "order" ? "notUsed" : "order";
+      if (!d.tb[targetLstName]) d.tb[targetLstName] = [];
+      const targetLst = d.tb[targetLstName];
+      d.tb[d.lstName].splice(d.index, 1);
+      if (d.lstName == "order") targetLst.unshift(d.key);
+      else targetLst.push(d.key);
+      self.init({
+        sortOptions: {
+          [s.sortSamplesBy]: self.activeOption
+        }
+      });
+    });
+    div.append("div").style("display", "inline-block").style("cursor", "pointer").style("width", "12px").style("height", "12px").style("margin-right", "3px").style("background-color", d.cls.color);
+    div.append("span").style("cursor", "pointer").style("text-decoration", d.filterByClass[d.key] == "case" ? "line-through" : "").html(d.cls.label + (d.filterByClass[d.key] ? " (<i>not used since this value is hidden</i>)" : ""));
+    const toggle = div.append("div").style("display", "inline-block").style("width", "12px").style("cursor", "pointer").style("opacity", 0).style("color", d.lstName == "order" ? "red" : "green").html(d.lstName == "order" ? "&cross;" : "&check;");
+  }
+  function trackDraggedValue(event, d) {
+    event.stopPropagation?.();
+    dragged.type = "value";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.tiebreaker = event.target.closest("tr").__data__;
+    dragged.tbIndex = dragged.sectionData.tiebreakers.indexOf(dragged.priorityIndex);
+    dragged.order = dragged.tiebreaker.order;
+  }
+  function highlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    if (d.tb != dragged.data.tb) return;
+    event.preventDefault();
+    const i = dragged.order.indexOf(d);
+    select_default(this).style("border", "2px solid blue");
+  }
+  function unhighlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value") return;
+    event.preventDefault();
+    select_default(this).style("border", "none");
+  }
+  function adjustValueOrder(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    event.preventDefault();
+    const s2 = self.settings;
+    dragged.data.tb[dragged.data.lstName].splice(dragged.data.index, 1);
+    d.tb[d.lstName].splice(d.index, 0, dragged.data.key);
+    const j = s2.hiddenVariants.indexOf(dragged.data.key);
+    const hiddenVariants = structuredClone(s2.hiddenVariants);
+    const filterByClass = structuredClone(s2.filterByClass);
+    if (j != -1) {
+      hiddenVariants.splice(j, 1);
+      filterByClass[dragged.data.key] = false;
+    }
+    self.init({
+      hiddenVariants,
+      filterByClass,
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function showNotUsedValues(event, tb) {
+    event?.stopPropagation();
+    const availDiv = tip.clear().d.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-vals").style("margin-top", "3px").style("vertical-align", "top").style("padding-left", "12px");
+    availDiv.selectAll("div").data(
+      tb.notUsed.map((key, index) => ({
+        lstName: "notUsed",
+        key,
+        cls: mclass[key],
+        tb,
+        dragstart: trackDraggedValue,
+        dragover: highlightValue,
+        dragleave: unhighlightValue,
+        drop: adjustValueOrder,
+        filterByClass: s.filterByClass,
+        index
+      }))
+    ).enter().append("div").style("display", "block").each(setValueDiv);
+    tip.showunder(event.target);
+  }
+  function apply() {
+    parent.app.tip?.hide();
+    parent.app.dispatch({
+      type: "plot_edit",
+      id: parent.id,
+      config: {
+        settings: {
+          matrix: {
+            sortOptions: {
+              [s.sortSamplesBy]: self.activeOption
+            }
+          }
+        }
+      }
+    });
+  }
+  function undoMouseoverHighlights() {
+  }
+  function handleSelectedTerms(td, tr) {
+    if (!parent.selectedTermsToSortAgainst?.length) {
+      td.html(`Click on a matrix row label and the left triangle to add an entry here`);
+      return;
+    }
+    const selectedTerms = parent.selectedTermsToSortAgainst.map((t) => {
+      return {
+        t,
+        label: t.tw.term.name + (t.tw.term.type == "geneVariant" ? " alterations" : " values")
+      };
+    });
+    const tbody = select_default(tr.node().parentNode);
+    tbody.selectAll("tr").remove();
+    tbody.selectAll("tr").data(selectedTerms).enter().append("tr").selectAll("td").data((d, i) => [
+      { label: i + 1, textAlign: "center", cursor: "", t: d.t },
+      { label: d.label, textAlign: "left", cursor: "" },
+      {
+        label: "Delete",
+        textAlign: "center",
+        cursor: "pointer",
+        click: parent.unsortSamplesAgainstTerm,
+        data: d
+      }
+    ]).enter().append("td").style("text-align", (d) => d.textAlign).style("cursor", (d) => d.cursor).html((d) => d.label).on("click", (event, d) => d.click?.(event, d));
+  }
+  self.init();
+  self.api = {
+    main: self.init,
+    destroy: () => {
+      opts.holder.selectAll("*").remove();
+    }
+  };
+  if (opts.debug) self.api.Inner = self;
+  return self.api;
+}
+
+export {
+  getSorterUi
+};
+//# sourceMappingURL=chunk-EYKJQJ7R.js.map

package/dist/chunk-FE5TCBIT.js

@@ -0,0 +1,30 @@
+import {
+  dtTermTypes,
+  migrateLegacyTvsOrigins
+} from "./chunk-JHLF2ZC2.js";
+
+// filter/rehydrateFilter.js
+function rehydrateFilter(filter, vocabApi, proms = []) {
+  if (Object.isFrozen(filter)) throw "filter obj is frozen, unable to rehydrate and modify";
+  if (filter.type == "tvslst") {
+    for (const f of filter.lst) rehydrateFilter(f, vocabApi, proms);
+  } else if (filter.type == "tvs") {
+    if (typeof filter.tvs?.term != "object") throw "a tvs lacks structure of .tvs.term{}";
+    if (dtTermTypes.has(filter.tvs.term.type)) migrateLegacyTvsOrigins(filter.tvs);
+    if (filter.tvs.term.id && !filter.tvs.term.name) {
+      proms.push(
+        vocabApi.getterm(filter.tvs.term.id).then((term) => {
+          filter.tvs.term = term;
+        })
+      );
+    }
+  } else {
+    throw `cannot rehydrate filter.type='${filter.type}'`;
+  }
+  return proms;
+}
+
+export {
+  rehydrateFilter
+};
+//# sourceMappingURL=chunk-FE5TCBIT.js.map

package/dist/chunk-FJ2JV2VK.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-4TJO2DGU.js";
+import {
+  contigNameNoChr2
+} from "./chunk-WJLRU5OF.js";
+
+// tracks/hic/data/parseData.ts
+async function hicParseFile(hic, debugmode, errList = []) {
+  if (debugmode) window["hic"] = hic;
+  if (hic.tklst) {
+    const lst = [];
+    for (const t of hic.tklst) {
+      if (!t.type) {
+        errList.push("type missing from one of the tracks accompanying HiC");
+      } else {
+        t.iscustom = true;
+        lst.push(t);
+      }
+    }
+    if (lst.length) {
+      hic.tklst = lst;
+    } else {
+      delete hic.tklst;
+    }
+  }
+  if (hic.enzyme) {
+    if (hic.genome.hicenzymefragment) {
+      let frag = null;
+      for (const f of hic.genome.hicenzymefragment) {
+        if (f.enzyme == hic.enzyme) {
+          frag = f;
+          break;
+        }
+      }
+      if (frag) {
+        hic.enzymefile = frag.file;
+      } else {
+        errList.push("unknown enzyme: " + hic.enzyme);
+        delete hic.enzyme;
+      }
+    } else {
+      errList.push("no enzyme fragment information available for this genome");
+      delete hic.enzyme;
+    }
+  }
+  try {
+    if (hic.sv && hic.sv.file) {
+      const re = await dofetch(hic.hostURL + "/textfile", {
+        method: "POST",
+        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
+      });
+      const data2 = re.json();
+      const [err2, header, items] = parseSV(data2.text);
+      if (err2) throw { message: "Error parsing SV: " + err2 };
+      hic.sv.header = header;
+      hic.sv.items = items;
+    }
+    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
+    if (data.error) {
+      errList.push(data.error);
+      return;
+    }
+    const err = hicparsestat(hic, data.out);
+    if (err) throw { message: err };
+  } catch (err) {
+    errList.push(err.message || err);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+  }
+  return hic;
+}
+function parseSV(txt) {
+  const lines = txt.trim().split(/\r?\n/);
+  const [err, header] = parseSVheader(lines[0]);
+  if (err) return ["header error: " + err];
+  const items = [];
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line[0] == "#") continue;
+    const [e, m] = parseSVline(line, header);
+    if (e) return ["line " + (i + 1) + " error: " + e];
+    items.push(m);
+  }
+  return [null, header, items];
+}
+function parseSVheader(line) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_A missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_B missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("strand_a", "orta", "orienta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb", "orientb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("numreadsa");
+  if (i != -1) header[i] = "reads1";
+  i = htry("numreadsb");
+  if (i != -1) header[i] = "reads2";
+  return [null, header];
+}
+function parseSVline(line, header) {
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) return ["missing chr1"];
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) return ["missing chr2"];
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  if (!m.position1) return ["missing position1"];
+  let v = Number.parseInt(m.position1);
+  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
+  m.position1 = v;
+  if (!m.position2) return ["missing position2"];
+  v = Number.parseInt(m.position2);
+  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
+  m.position2 = v;
+  if (m.reads1) {
+    v = Number.parseInt(m.reads1);
+    if (Number.isNaN(v)) return ["reads1 invalid value"];
+    m.reads1 = v;
+  }
+  if (m.reads2) {
+    v = Number.parseInt(m.reads2);
+    if (Number.isNaN(v)) return ["reads2 invalid value"];
+    m.reads2 = v;
+  }
+  return [null, m];
+}
+function hicparsestat(hic, j) {
+  if (!j) return "cannot stat hic file";
+  hic.normalization = j.normalization;
+  hic.version = j.version;
+  if (!j.Chromosomes) return "Chromosomes not found in file stat";
+  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
+  if (j.chrorder.length == 0) return ".chrorder[] empty array";
+  hic.chrorder = j.chrorder;
+  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
+  hic.bpresolution = j["Base pair-delimited resolutions"];
+  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
+  hic.fragresolution = j["Fragment-delimited resolutions"];
+  const chrlst = [];
+  for (const chr in j.Chromosomes) {
+    chrlst.push(chr);
+  }
+  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
+  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
+  if (nochrcount > 0) {
+    hic.nochr = true;
+    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
+  }
+  hic.chrlst = [];
+  for (const chr of hic.genome.majorchrorder) {
+    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
+    if (chrlst.indexOf(c2) != -1) {
+      hic.chrlst.push(chr);
+    }
+  }
+}
+function hicparsefragdata(items) {
+  const id2coord = /* @__PURE__ */ new Map();
+  let min = null, max;
+  for (const i of items) {
+    if (!i.rest || !i.rest[0]) {
+      return ["items[].rest data problem"];
+    }
+    const id = Number.parseInt(i.rest[0]);
+    if (Number.isNaN(id)) {
+      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
+    }
+    id2coord.set(id, [i.start, i.stop]);
+    if (min == null) {
+      min = id;
+      max = id;
+    } else {
+      min = Math.min(min, id);
+      max = Math.max(max, id);
+    }
+  }
+  return [null, id2coord, min, max];
+}
+
+export {
+  hicParseFile,
+  hicparsestat,
+  hicparsefragdata
+};
+//# sourceMappingURL=chunk-FJ2JV2VK.js.map

package/dist/chunk-FZYVPRVQ.js

@@ -0,0 +1,38 @@
+import {
+  plotColor
+} from "./chunk-WJLRU5OF.js";
+
+// plots/violin/settings/defaults.ts
+function getDefaultViolinSettings(app, overrides = {}) {
+  const defaults = {
+    orientation: "horizontal",
+    rowlabelw: 250,
+    brushRange: null,
+    //object with start and end if there is a brush selection
+    svgw: 500,
+    // span length of a plot/svg, not including margin
+    datasymbol: "rug",
+    radius: 10,
+    axisHeight: 60,
+    rightMargin: 50,
+    lines: [],
+    isLogScale: false,
+    // false: linear scale, true: log scale
+    rowSpace: 10,
+    medianLength: 7,
+    medianColor: "#FF0000",
+    medianThickness: 3,
+    ticks: 15,
+    defaultColor: plotColor,
+    method: 0,
+    orderByMedian: false,
+    showStats: true,
+    showAssociationTests: true
+  };
+  return Object.assign(defaults, overrides);
+}
+
+export {
+  getDefaultViolinSettings
+};
+//# sourceMappingURL=chunk-FZYVPRVQ.js.map